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Not exactly sure on how " a zeotropic is expected to have bubbles in a sight glass because they are known for fractionization"? Over i'm guessing a pure blend? maybe he meant the Glide? Fractionization with lets say hmm. R410a
a Glide of 0.2 Very minimum very low chance of fractionization to ever be noticed being that the 2 refrigerants R32 and R125 act so closely to one another, loosing the moelcules from one substance more than the other you'll
never see the difference. now 407C on the other hand with a Glide of 10 compound make up of R32/125/134A the molecules from the R32 and the R125 in vapor form move much faster then the molecules of 134A therefor if there was a leak it would be more likely to loose the R32 and R125 before it would loose the 134A. Causing the system pressures to favor the refrigerant that has the most is in the system. Point being because it is a blended refrigerant does not mean that bubbles in a sight glass are expected.
SH and SC are great tools. Not your only tools. Charge by manufacturers specs and you cannot go wrong. Knowing the ID WB and OD DB are just as important as SH and SC.

I use a yellow jacket refrigeration analyzer for all my refrigeration work. It only takes seconds to put it on. All units we install comes with a 10 year parts and labor warranty and with these gauges I record a proper vacuum and run operation. I cant afford call backs so we do our best to prevent them. I also do warranty work for York so I send them PDF files on the systems as to what we find.

Low sub cool and high super heat yes can be undercharged, dirty coil, dirty filter... evaporator is not picking up any heat.

If you have a txv and it has high superheat after 15 minutes of operation, Lets leave diagnostics to onsite techs. This is not a DIY site